Note: see recipe notes below about cookies not spreading or cookie dough being dry.
Preheat the oven to 350°F. Line 2 baking sheets with parchment paper or silicone baking mats. Set aside.
Brown the butter: For a detailed tutorial, see this post on how to brown butter. Allow the butter to cool slightly, ~10-15 minutes. 12 Tbsp. unsalted butter
Beat in the sugars into the brown butter using a hand mixer.
1 cup dark brown sugar, packed, 1/2 cup granulated sugar
Add in eggs, milk and vanilla. Beat again.
1 large egg, 1 large egg yolk, 2 Tbsp. whole milk, 1 Tbsp. pure vanilla extract
Sift in the dry ingredients and fold just until combined. (Keep stirring, the cookie dough will come together!)
2 2/3 cups all purpose flour, 1 tsp. salt, 1 tsp. baking soda, 1/2 tsp. baking powder
Fold in only 3/4 cup of the chocolate chunks (we will use the rest of the chunks to decorate the tops). Dough should feel like cookie dough, if it feels dry still add a splash more milk and stir to combine.
2, 4 oz. bars semi sweet chocolate, chopped, divided
Dunk a cookie dough ball in the remaining chopped chocolate so the pieces cover the tops of the cookie dough balls. Press chocolate into cookie slightly just to be sure it sticks. You can slightly flatten them to get a good surface so the chocolate sticks if thats easier! Repeat with remaining cookie dough balls and place 6 cookies on a baking sheet at a time. (Should yield ~22 cookies)
Bake for 10-11 minutes (I like to go slightly underbaked for a delicious chewy cookie, the edges should be a light golden brown and centers still a little gooey looking, they will continue to bake on baking sheet when removed from oven). Swirl a cup around the edges of the cookies to give them a perfect circular look if needed.
Rest on cookie sheet just 2-3 minutes then gently transfer to a cooling rack to cool and garnish with flaky sea salt if desired.